|
| Status |
Public on Nov 10, 2023 |
| Title |
RNA-Seq F1_parent_Diff10_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
mixed neural differentiated cell progeny
|
| Organism |
Mus musculus |
| Characteristics |
strain: 129S1/Cast F1 Hybrid
clone: Clone 5B
cell type: mixed neural differentiated cell progeny
genotype: Sox2-mCherry (129)
treatment: no deletion
|
| Treatment protocol |
Enhancer deleted clones contain heterozygous or homozygous deletions of enhancer clusters within the study. Deletions were generated in mouse embryonic stem cells using Cas9 endonuclease and guide RNA.
|
| Growth protocol |
All neural stem and progenitor cells were maintained on poly-d-lysine and laminin coated plates in N2B27 media supplemented with EGF and bFGF. To induce differentiation of NSPCs into neurons and astrocytes, cells were cultured in complete NeuroCult™ Differentiation Kit (Mouse & Rat) medium for 10 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using silica-membrane RNeasy columns (Qiagen) and treated with TURBO DNase (Thermo Fisher) prior to library construction
Total ribo-depleted RNA-seq libraries were prepared for Illumina HiSeq2500 125bp paired-end sequencing
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
F1_parent_Diff10_rep1
|
| Data processing |
Reads were trimmed using fastp/0.20 (https://github.com/OpenGene/fastp) with standard settings.
Reads were aligned to mm10 using STAR/2.7.9a (https://github.com/alexdobin/STAR) with the following options: --alignEndsType Local --outFilterMultimapNmax 20
The alignment BAM files for each biological replicate were used to create track formatted bedGraph files that were normalized to counts per million mapped reads (CPM) using Deeptools bamCoverage (https://github.com/deeptools/deepTools)
Assembly: mm10
Supplementary files format and content: bedGraph
|
| |
|
| Submission date |
Jul 19, 2023 |
| Last update date |
Nov 10, 2023 |
| Contact name |
Jennifer Mitchell |
| E-mail(s) |
ja.mitchell@utoronto.ca
|
| Phone |
4169786711
|
| Organization name |
University of Toronto
|
| Department |
Cell and Systems Biology
|
| Street address |
25 Harbord Street
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5S 3G5 |
| Country |
Canada |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE237775 |
Bulk RNA-seq of mouse neural stem and progenitor cells (NSPC) derived from embryonic stem cells, with allele-specific deletions of a Sox2 enhancer cluster |
| GSE237778 |
SuperSeries=Mouse neural stem and progenitor cells (NSPC) derived from embryonic stem cells, with biallelic Sox2 enhancer cluster deletions |
|
| Relations |
| BioSample |
SAMN36632481 |
| SRA |
SRX21084688 |
